Tree Genetics and Molecular Breeding 2024, Vol.14, No.3, 106-118 http://genbreedpublisher.com/index.php/tgmb 108 2019). These technologies hold the potential to detect all types of genomic variations, including single nucleotide polymorphisms (SNPs), indels, copy number variations, and chromosomal rearrangements, with high precision (Anderson, 2018). Advancements in in situ nucleic acid sequencing and microscopy-based sequencing are also on the horizon, offering new avenues for spatially resolved genomic analyses. These techniques could provide detailed insights into the spatial organization of genomes within tree tissues, enhancing our understanding of gene regulation and cellular differentiation (Kumar et al., 2019). Furthermore, the development of more efficient and scalable sequencing platforms will likely reduce costs and increase accessibility, enabling broader applications in tree genomics. This includes the potential for real-time sequencing in the field, which could revolutionize tree breeding programs and conservation efforts by providing immediate genetic information (Anderson, 2018; Kumar et al., 2019). 3 Genomic Diversity Across Tree Species 3.1 Comparative genomic analysis of broadleaf and conifer trees Comparative genomic analysis between broadleaf and conifer trees reveals significant differences in their genomic structures and evolutionary adaptations. For instance, spruces, which are coniferous trees, possess very large and repetitive genomes that complicate comparative analysis. However, recent studies have provided more contiguous genome assemblies for various spruce species, such as Engelmann spruce, Sitka spruce, and white spruce. These genomes exhibit structural similarities but also show distinct patterns of gene family expansions and rapidly evolving genes, which are linked to ecological adaptations (Figure 1) (Gagalova et al., 2022). In contrast, broadleaf trees like European beech (Fagus sylvatica) have been studied for their phenology-related genes, revealing significant SNP diversity associated with local adaptations to climatic variables (Meger et al., 2021). This comparative approach underscores the unique evolutionary paths and adaptive strategies of broadleaf and conifer trees. Gagalova et al. (2022) focuses on the genomic mapping and hybrid analysis of various spruce species, specifically examining the genetic composition and evolutionary relationships within the Picea genus. By integrating genetic maps and genome assemblies, researchers achieved high synteny across different spruce species, validating the accuracy of the genomic scaffolding process. The study also confirmed the hybrid nature of the interior spruce genotype PG29, revealing predominant contributions from white spruce, along with significant genetic input from Engelmann and Sitka spruces. These findings are essential for understanding the complex hybridization events and genetic diversity in spruce species, providing valuable insights for tree breeding, conservation strategies, and the broader study of conifer genomics. 3.2 Insights into genetic variability and its ecological significance Genetic variability within tree species is crucial for their adaptation to changing environments. The GenTree project, for example, has documented extensive intra- and interspecific leaf trait variability in seven European tree species, including both conifers and broadleaves. This variability is linked to resource acquisition and conservation, highlighting the ecological significance of genetic diversity in response to environmental gradients (Benavides et al., 2021). Additionally, studies on European beech have shown that genetic variation closely mirrors geographic distribution, with adaptive variation involving thousands of sequence variants across the genome. This polygenic architecture is essential for predicting future maladaptation under climate change conditions. Such insights into genetic variability are vital for understanding how tree species can maintain ecosystem stability and resilience. 3.3 Case studies: unique genomic adaptations in tree species Several case studies illustrate unique genomic adaptations in tree species. For instance, the subtropical oak Quercus acutissima has shown significant genomic and phenotypic differentiation between eastern and western populations. This differentiation is associated with environmental factors such as precipitation, indicating local adaptation (Gao et al., 2020). Another example is the development of a high-throughput SNP array for Araucaria
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